In season 2:
In the Halloween episode while Buffy was being a damsel in distress Willow took charge (before finding Giles). Also Willow was the leader in "The Dark Age" - she came up with the plan to get the spirit off Jenny. In Becoming part 2, while Willow is at the hospital she is the one who tells Xander to go to Buffy and instructs Cordy and Oz to help with the spell.
I don't think the Scoobies take leadership roles in season 3. Unless you count Xander commanding the high school "army" in Graduation Day part 2.
Doesn't Willow in season 5 take Buffy's place while she's catatonic? And in season 6, when Willow is dark - but not too dark yet - she goes after Warren, while Buffy and Xander trail behind her (before the realize Willow she wants to kill him). Is Willow always the back-up leader if Buffy and Giles are unavailable? In Bargaining, while Buffy's still death and Giles is in London, she's the one in charge.
I can't think of anything else. Hope this helped.